Comparative transcriptomics of tropical woody plants supports fast and furious strategy along the leaf economics spectrum in lianas

Lianas, climbing woody plants, influence the structure and function of tropical forests. Climbing traits have evolved multiple times, including ancestral groups such as gymnosperms and pteridophytes, but the genetic basis of the liana strategy is largely unknown. Here, we use a comparative transcriptomic approach for 47 tropical plant species, including ten lianas of diverse taxonomic origins, to identify genes that are consistently expressed or downregulated only in lianas. Our comparative analysis of full-length transcripts enabled the identification of a core interactomic network common to lianas. Sets of transcripts identified from our analysis reveal features related to functional traits pertinent to leaf economics spectrum in lianas, including upregulation of genes controlling epidermal cuticular properties, cell wall remodeling, carbon concentrating mechanism, cell cycle progression, DNA repair and a large suit of downregulated transcription factors and enzymes involved in ABA-me..., Sample Set
The Luquillo transcriptomic set included six lianas (DIO) Dioscorea poligonoides (Dioscoreaceae), (HET) Heteropterys laurifolia (Malpighiaceae), (PAU) Paulinia pinnata (Sapindaceae), (SEC) Securidaca virgata (Polygonaceae), (SMI) Smilax coriaceae (Smilaceae), (DOL) Dolichandra unguis-cati (Bignoniaceae). We also included four more liana species from National Center for Biotechnology Information’s Sequence Read Archive (NCBI-SRA) and One Thousand Plant Genomes (1KP) dataset (Matasci et al. 2014, 1KP 2019) with the following accessions (GNE) Gnetum montanum (Gnetaceae) SRR5908685, (SMISIE) Smilax sieboldii (Smilacae) SRR5134200, (PASCAE) Passiflora caerulea (Passifloraceae) 1KP id:SIZE, (SCHPAR) Schlegelia parasitica (Schlegeliaceae) 1KP id:GAKQ. A full list including non-liana species can be found in the supplementary (SI Appendix Dataset S1, SI Appendix Fig. S1,).
Sample Collection and RNA Library Construction
To analyze the transcriptomes, we chose healthy and fully develope..., The dataset in this submission is in three parts:
[1] A multi-tab Excel spreadsheet that includes species list; analysis results of QUAST quality control; validation of assembled transcriptomes by Bowtie2 alignments; measures of completeness by BUSCO analysis; results of gProfiler analysis for enriched genes, domains and categories.
[2] A Cytoscape generated network used in Figure 1. For reproducible results we recommend selecting \"Ripple\" as the visual style and \"Preset\" as layout to retain formatting used in the manuscript. Source Cytoscape file (Liana-L5-L2.DRYAD.cys).
[3] Four fasta formatted files for each species:
(a) TRINITY assembled unfiltered transcripts (SPECIES.Trinity.fasta).
(b) EnTAP filtered transcripts for non-plant contaminant sequences (SPECIES.decon.fasta). 
(c) EnTAP filtered translated/frame-selected full-length protein sequences (SPECIES-fl-protein.fasta). 
(d) EnTAP filtered full-length transcript nucleotide sequences (SPECIES-fl-nt.fasta).